Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

Cichlid fish of the genus Oreochromis form the basis of the global tilapia
aquaculture and fisheries industries. Broodstocks for aquaculture are
often collected from wild populations, which in Africa may be from
locations containing multiple Oreochromis species. However, many species
are difficult to distinguish morphologically, hampering efforts to
maintain good quality farmed strains. Additionally, non-native farmed
tilapia populations are known to be widely distributed across Africa and
to hybridize with native Oreochromis species, which themselves are
important for capture fisheries. The morphological identification of these
hybrids is particularly unreliable. Here, we describe the development of a
single nucleotide polymorphism (SNP) genotyping panel from whole-genome
resequencing data that enables targeted species identification in
Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs
based on FST outliers performs comparably to whole genome resequencing in
distinguishing species and identifying hybrids. We also show this panel
outperforms microsatellite-based and phenotype-based classification
methods. Case studies indicate several locations where introduced
aquaculture species have become established in the wild, threatening
native Oreochromis species. The novel SNP markers identified here
represent an important resource for assessing broodstock purity in
hatcheries and helping to conserve unique endemic biodiversity.